My InterpretationTo me this song is about intrusive thoughts, which is the psychiatric term for unwelcome, involuntary, or unpleasant thoughts, images, or ideas. Intrusive thoughts are often associated with obsessive-compulsive disorder and other personality and social disorders, but they are also something that all human beings experience from time to time. Fortunately they are short-lived experiences which most of us are able to cast out of our minds in 'just one second'.

The song is written from the perspective of a person whose mind is racing about as he reflects on past experiences, seemingly experiences from a relationship which is either struggling or has ended. But given the theme of intrusive thoughts, it is possible that the song's entire tone of dismay is itself an intrusive thought. It's a very complex and beautiful song when you think about it from this perspective.

In case my meaning is not clear, here is a more precise explanation:
In the first verse, the speaker recalls brief thoughts of wishing someone was dead (intrusive thought) and also a fear of himself being wished away by that person (intrusive thought). Then he says don't cry because it was just hypothetical. In the second verse he recalls an intense emotional feeling, brought on by something someone said, which took his breath away, but the feeling is broken by recollection of a time of perceived loneliness (intrusive thought). Again he says don't cry, it was hypothetical. In the last verse he expresses bittersweet but brief feelings of clarity and either dependency or devotion, but again these feelings are broken by that of isolation (intrusive thought). He finishes by saying one last time don't cry, because the tears are hypothetical. This entire sequence of feelings exists only in his mind, and so any tears shed by the listener/subject will fall alone inside his imagination.